Pilot
Pilot Flight 627 from Hamburg is caught in an electrical storm whilst in flight. Most of the cabin lights are off, and flashes of lightning illuminate the seated areas. Various passengers are speaking German. Elsewhere on the plane, a nervous-looking passenger cradles his head in his hands, his eyes wide. He sits back and takes a few breaths, then opens a briefcase and takes out a packet containing an insulin pen. Pinching a fleshy portion of his stomach between thumb and forefinger, he injects himself with the pen. The man beside him tries to reassure him that the storm is nothing to worry about and offers him some gum. The nervous passenger declines, takes a few more breaths, then then unfastens his safety belt, gets up, and starts walking up the aisle. A hostess sees him and goes after him. Once she reaches him he stops and turns with a look of horror on his face - the skin on his face and hands seems to be decaying rapidly and dissolving. Unable to control himself, he spits bodily fluid all over the hostess, who screams and turns to look at the other passengers. Everyone begins to panic as they realize their own flesh is degenerating as well. The hostess telephones the captain and tells him they have a problem. In the cockpit alarms are sounding. The co-pilot opens the door to find out what is causing all the noise from the cabin. He sees the passengers of the craft in their decayed state and stands in shock. The pilot asks him what is wrong, engaging the craft's auto-pilot system and turning to look at his co-pilot. The co-pilot turns as his own skin begins to decay, and lets out an agonized moan as the skin around his bottom jaw dissolves and begins to fall apart. The auto-pilot engaged, Flight 627 flies on through the storm. Olivia Dunham and John Scott lie in bed together. Olivia tells Scott that she would prefer not to be so secretive about their relationship. Scott remarks that their department would frown upon office romance, but reminisces about finding himself attracted to her for the first time. Olivia says that one of their co-workers, Charlie Francis, might know about their. Scott jokes that if Charlie knew he would transfer Charlie to another department. He tells Olivia that he loves her. Olivia smiles and kisses him, but the kiss is interrupted by Olivia's mobile phone vibrating. She takes the call, which is from one of her superiors, and hastily begins dressing. Once off the phone she tells Scott there has been an incident involving an international flight at Logan International Airport and that Charlie is on his way there. At Logan Airport, Boston, various emergency crews have gathered to surround flight 627, now out on the runway. Teams from various agencies – CDC, CIA, FBI – are gathered under marquees discussing the situation. Olivia arrives and is greeted by Charlie Francis, who informs her that the flight was from Hamburg, carried 147 passengers, contact with it was lost three hours into the flight, and that once the plane entered US airspace it was radio-silent and had to be escorted by two Navy F-18 jets. He tells her the pilots of the jets reported blood stains on the windows and no signs of life aboard the plane, but the plane was successfully landed by the autopilot system. Charlie said one of the agent checked inside through the window, and saw something, that made him to vomit everywhere. Scott arrives, talking on his mobile phone, assuring the caller that he'd “be happy to treat you as family too”. He greets Charlie and Olivia formally as “Agent Francis” and “Agent Dunham”. A black car pulls up at the airport checkpoint. The driver winds down his window, keeping his face in shadow, and asks what has happened. The guard at the gate informs him the runway is closed and tells him to move along. The driver leans out of the window to look, and he appears to be the nervous passenger from Flight 627, alive and well. He pulls back into the car and drives away. Special Agent Phillip Broyles arrives on the runway and briefs the gathered agents. He selects Scott and Charlie to enter the plane but after Olivia protests he allows her to board as well. All three FBI agents dress in HAZMAT suits and enter the plane. Inside they find the skinless corpses of the passengers and crew, and speculate as to whether the incident was a result of terrorist activity. At the Federal Building in Boston, the various agents are at work tracking down information about the flight. Televised news feeds in the background are reporting that the plane has been destroyed by fire under control of the CDC. Inside the main office, Broyles asks Olivia to follow a lead involving a sighting of “two middle-eastern men handing a white guy a briefcase”. Olivia protests but Broyles is insistent, and a vexed Olivia leaves the office. Olivia and Scott arrive at the place their suspect was sighted - the U-Case Storage facility in Back Bay, Massachusetts. Olivia complains that Broyles is mistreating her because she had his best friend jailed on a sexual assault charge. Scott tells her that Broyles is just jealous, and the two discuss their relationship again. Olivia explains that she was afraid of returning Scott's affection because of relationship difficulties in her past, but tells him she loves him too. The two kiss, and begin searching the area. After finding two empty canisters of ammonia in a dumpster they search the garages and discover animals in cages and extensive amounts of computer equipment. As Scott is searching one of the garages the door opposite opens and the driver of the black car from the airport emerges. He sees Scott and begins to run. Scott gives chase and calls Olivia, who joins the chase close behind. The suspect runs past a long stretch of garages then stops, turns and speed-dials a number on his mobile. Just as Scott levels a gun at him, with Olivia only a few yards behind, the garages on either side explode, engulfing Scott and throwing Olivia against a wall. She falls unconscious. Olivia wakes up in a hospital and goes to find Scott. A doctor informs her that while she was lucky to escape relatively unharmed, Scott has developed a tissue-damaging condition which is decaying his skin – just like the passengers of Flight 627. The hospital are keeping him in a state of drug-induced coma to slow the degeneration of his body. Olivia searches the FBI archives for anything that could present a solution to Scott's condition. She finds references to Walter Bishop, a former scientist who did research into tissue regeneration. She takes his file to Broyles, who notes that Bishop is in a psychiatric hospital and is only allowed visits from his next-of-kin. Olivia decides to follow it up to help Scott, and goes in search of Walter Bishop's son, Peter Bishop. Olivia tracks down Peter Bishop in Baghdad. Peter has just finished negotiating a business deal with two Iraqi oil merchants when Olivia approaches him and asks for his help in visiting his father, Walter. Peter refuses, unable to comprehend why Olivia would need Walter for anything and saying he would rather stay in Iraq than visit his father. Olivia explains that Walter may be able to save the man she cares about from dying, and Peter apologizes but refuses a second time, saying “we all care about someone who's dying”. Finally Olivia tells Peter she has his file, knows the reason for him being in Iraq, and threatens to let “certain people” know his whereabouts. Peter smiles and agrees to leave with Olivia. On the return flight to America, Peter questions Olivia about his father. Olivia explains that Walter's basement laboratory in Harvard was not used for developing toothpaste, as Peter had been told, but for experiments into Fringe science or “Pseudoscience”. Olivia lists the subjects covered by Fringe Science, a list which includes Mind Control, Teleportation, Astral Projection, Invisibility, Genetic Mutation and Reanimation. Peter interrupts, asking if she's labeling his father as Doctor Frankenstein. Olivia meets this question with a knowing silence. Olivia, escorted by Peter, goes to meet Walter Bishop. Peter elects to stay outside whilst Olivia interviews Walter, who initially greets her with the words “I knew someone would come, eventually”. At first he seems mentally disparate and distracted, sometimes answering her questions about Scott's condition directly but other times following his own train of thought. After repeated questioning he asks if he can see Peter. Peter grudgingly goes in to see his father. Walter tells his son he was expecting him to be fatter and attempts to check his pupils. Peter recoils and snaps at his father and Walter returns to talking about Scott, saying he cannot give an accurate judgment without seeing the damage first-hand. Peter must become Walter's legal guardian to sign him out of the hospital. He initially refuses but again Olivia threatens to call people who might be interested in his whereabouts. Peter reluctantly agrees, and Walter is signed out of the hospital – having first given himself a thorough shave. Whilst driving to the hospital where Scott is being treated, Walter explains that very few people knew about his research – the only other who had full understanding being William Bell. Peter informs his father that Bell went on to be the founder of Massive Dynamic, a multi-million-dollar corporation, and remarks upon the irony of one scientist becoming a millionaire whilst the other becomes a mental patient. Walter accompanies this with a yelp, declaring that he has just pissed himself. As the car drives on it passes a poster advertising Massive Dynamics, bearing the slogan “What do we do? What don't we do.” Back at the hospital, Olivia tells Charlie that the CDC have confirmed the incident on the plane was caused by a synthetic compound, but complains this is of no help to her investigation. She asks Charlie to set up a meeting with William Bell. Walter examines Scott, whose condition is only getting worse, and picks up a scalpel – to the initial horror of Peter. Walter calmly takes a skin sample from Scott and says he must take it to his old Laboratory. Olivia tells him the lab has been shut down and Walter takes the news very angrily, pushing over a hospital cart and storming out. Olivia goes to see Broyles to get Walter's lab reopened. Broyles hints that he knows about the relationship between Scott and Olivia, but Olivia ignores this and tells him to get the lab reopened. Once back at the lab, Walter begins requesting equipment – including raw materials, blood samples from anonymous donors, a NASA-grade micro-organism detector, and a pure-bred cow. Peter explains that cows bear a genetic resemblance to humans that differs only by a couple of lines. While the lab is being restocked and cleaned, Olivia looks over the photographs from Flight 627. Peter brings her a coffee and asks her what was in the file the FBI had on him. She hesitates and does not answer, and Peter realises she has been bluffing. Despite this he reveals he owes large sums of money to a gangster named Big Eddie. Walter explains that a chemical compound similar to the Flight 627 chemical was developed for use in the Vietnam war and that the version used on the plane was derived from that research. Scott, however, has reacted to the raw ingredients of the compound and not the compound itself so he cannot produce a cure for Scott without first knowing what substances were used. Walter predicts Scott has only 24 hours left before his body ceases to supply his brain with oxygen. With the garages containing the ingredients destroyed, and Scott being the only one who has seen the suspect, Olivia is ready to give up until Walter suggests a Synaptic Transfer forming a mental link between her mind and Scott's mind so she can use his mental picture of the suspect to track him down. Walter explains it can be used even to gain information from people who have been dead for up to six hours. Despite this being a dangerous procedure, Olivia agrees. Scott is brought to the lab, Olivia's assistant Astrid Farnsworth joins them and the equipment is set up for the Synaptic Transfer. Charlie arrives to bring word on the meeting with William Bell – he is out of town and it will be 48 hours before the FBI have the jurisdiction to do anything about it. Charlie is shocked by the procedure Olivia is about to undergo and warns her to be careful. Olivia strips down to her underwear whilst Walter and Peter anesthetize her, attach electrodes to her and inject her with a mixture of different drugs. Olivia begins to lose consciousness as the pair of them lower her into the lab's water tank. Before they close the tank doors, Walter tells her it is good to feel like someone trusts him again. Walter explains to Astrid and Peter that the process should synchronize Olivia and Scott's brain patterns, allowing them to communicate subconsciously. The three wait for the process to take effect. As her mind synchronizes with Scott's, Olivia finds herself wearing a long dress and standing in a scrap yard. Someone walks behind her but is gone when she turns around. Looking up into the sky, she sees an object she identifies as her uncle's kayak, and questions why it is there. The scene changes and she is standing in a room with a flowered rug, a doll's house, a bed and a chair. The scene changes again and she is standing in a graveyard. Someone walks behind her again, and she turns. This time she finds John Scott standing opposite her. Walter observes that their brain patterns have synchronized. Olivia and Scott meet in a desert-like landscape with a checkered floor and the FBI logo stamped in the middle. They kiss passionately and Olivia tells Scott he was hurt. He cannot remember and that he feels cold. She asks him to remember what he saw and to show her the suspect's face so she can save him. She sees the events of the garage search from Scott's perspective and the suspect's face is shown to her. Peter and Walter open the tank and pull her out just as she awakens from her drug-induced sleep, with the suspect's face fresh in her mind. At the Federal Building Olivia puts together a reconstruction of the suspect's face. Whilst the reconstruction is being cross-referenced with the FBI databases, one of the team brings over a photograph a passenger from Flight 627 – the nervous-looking passenger, identified as Morgan Stieg. Looking through his records, they discover his identical twin brother Richard Steig, and the name of his last known employer – Massive Dynamic. Olivia visits Massive Dynamic hoping to talk to William Bell. Instead she is met by Nina Sharp, an Executive Director. Olivia explains that Richard Stieg may have stolen the research for the Flight 627 compound from Massive Dynamic, and that the chemical was brought on-board in his brother's insulin pen and became an airborne toxin which eradicated itself after destroying the passengers of the plane. Nina asks an assistant to assemble a file on Stieg and tells Olivia he was caught trying to sneak out with classified information. She says his contract was terminated immediately so the company have done all they can, and threatens Olivia with legal action if any bad word about the company is brought into the public domain. She goes on to say that she literally owes Massive Dynamic her life. Having developed cancer some years ago, she had to have her arm amputated; the machines responsible for detecting the disease and operating on her were designed by Massive Dynamic, and William Bell himself designed a replacement robotic arm, which she reveals by removing a flesh-toned glove from her right arm. Her assistant returns with the file and she gives it to Olivia, asking if she thinks Stieg may be “part of The Pattern”. Olivia does not know what The Pattern is, and Nina says she cannot not reveal anything more, only wishing Olivia good luck and telling her to be careful. Olivia calls Peter at the lab, asking him to bring Walter and meet her at Stieg's address. When they arrive an FBI team are already waiting to enter the building. They break into Stieg's flat and begin checking the rooms. Initially they find nothing, but Olivia discovers a trapdoor to a cellar that houses similar equipment to the U-Case garages. Stieg is nowhere to be seen. Walter is waiting outside in a car with Peter and asks to check his blood pressure, telling him his skin tone suggests he may be suffering from Hypertension. Peter protests that there are no visible symptoms of hypertension. Walter asks his son not to send him back to the psychiatric hospital after Scott has been cured, saying that he has already endured enough punishment. Peter sees Stieg exit the building by a back door and run away. He gives chase, with Olivia soon appearing close behind. Olivia chases Stieg up fire escapes, through a building, across rooftops and finally back down into the street, where he is tackled by Peter. Olivia catches up, puts a gun to his head and demands the information. Back at the lab, Walter and Peter argue about the formula they should apply to Scott's blood to reverse the contagion. They conclude that any antidote would result in a shock to the bloodstream and there is no way of applying it, but Olivia suggests they use the FBI's store of agents' blood samples to transfuse the antidote intravenously into his body. While the two of them set to work curing Scott, Olivia sits outside and talks to Broyles, who reveals the incident on Flight 627 is part of a series of paranormal events being labeled as The Pattern; 36 recorded incidents of a paranormal nature had occurred in the previous nine months. He gives examples: 47 children who disappeared in 1998 were found a few months previous to the present day, halfway around the world, and with no visible signs of having aged at all; a low-flying plane in Sri Lanka emits a high frequency sound which blows out any nearby windows, then an hour later an earthquake measuring 8.7 on the Richter scale hits, causing a tsunami which wipes out 83,000 people in the area; a hospital patient emerges from a coma and begins writing down a series of numbers, all of which correspond exactly to real-time coordinates of US military ships in the south pacific. Broyles describes it “as if someone conducting experiments, but with the whole world as a lab”. Olivia does not want to get involved, saying she only wants things back to how they were before, but Broyles tells her he thinks that may be impossible. Walter and Peter finish administering their cure. Scott soon returns to consciousness, and is transferred back to the hospital. While there, Olivia checks on Richard Stieg, asking why he would sacrifice his own brother and why he would sell his work. Stieg replies that he wasn't selling it and that he can prove he was threatened by someone from the FBI office. He tells Olivia there is a recording buried under a trash can by his house. She finds it, plays the recording and hears Richard being threatened over the phone by a man who finishes the conversation by saying “Let me assure you we'd be happy to treat you as family too”. Realizing those were Scott's final words as he stepped onto the runway at Logan Airport, Olivia frantically calls the hospital. Scott, acting alone, visits the room where Stieg is being held. He takes the pillow from under Stieg's head and suffocates him with it. Olivia calls Charlie and requests Scott be placed under guard and to check on Stieg. Charlie discovers Stieg has been killed and tries to get the hospital locked down. Olivia arrives just to see Scott fleeing in a blue SUV. She gives chase in her car and calls for police assistance. She manages to draw level with Scott, who attempts to ram her off the road. She brakes, forcing him to swerve into a maintenance ramp by the side of the road; his car overturns and he crawls from the wreckage with severe injuries to his head. Olivia runs over to check him and he asks her to question why Broyles sent her to the storage facility. She asks him who he is really working for but he does not answer; he finally succumbs to his head injuries and dies in her arms. An unspecified amount of time later, Charlie and Olivia are traveling in a car. Charlie tells Olivia that he knew about her relationship with Scott, muses on the protecting people from dangers of today's society, and claims the FBI are obsolete now that corporations have higher clearance than they do and they are barely briefed on half the incidents they investigate. Returning to Harvard, Olivia meets Walter and Peter outside. She speaks to Peter, asking him to remain in Boston since Walter has to stay to help the FBI explain The Pattern. He says that all his instincts tell him to leave Boston, but ultimately he decides to stay. At a facility that looks much like the Massive Dynamic building we saw earlier, a man is wheeling a body on a trolley through a white corridor. Nina Sharp walks up to the trolley and removes the cover from the body; it is John Scott. She asks how long Scott has been dead. The assistant replies he has been dead for nearly five hours, and Nina simply responds: “Question him”.